Hi All:
Compressed files used to be decompressed in galaxy after uploading. Recently, the compressed files (gz files) are failed to be decompressed after uploaded into Galaxy. Is it a common problem or just happened to me? Do I need to unzip files before uploading or manually decompress files using some galaxy tools? Thanks!

They way it works now is that .gz files do not uncompress on upload but rather on tool run.
You can now select the fastq.gz files as inputs for tools that expect fastq and Galaxy will uncompress them before sending to the tool. See example below.

We will release Galaxy 17.01 (which contains this feature) in the upcoming weeks. If you don't want to wait you can clone it already from our repo (branch release_17.01) but beware that there might be more bugs than usual since we are still testing it.

I can wait, but this is great - it is a long-desired feature to be able to handle compressed read data transparently. Is this a fundamental datatype (i.e. can it be set as an output format for tools that can natively write compressed fastq or which we can pipe through gzip when history size is more important than speed of execution)?

I was hoping that what you described was that case. But when I uploaded my fastq.gz files and run Bowtie with them as input (this is a part of a workflow), Bowtie failed to run and this is the error message:

If I'm not mistaken, since galaxy version 17.01, when uploaded the fastq.gz file, it should not uncompress. Galaxy will uncompress the file when it is on tool run (I re-tested it by uploaded fastq.gz files to see if any error occurred or it changed as fastqsanger but I did not get any). This way, the user's quota space can be saved when dealing with files with large size.

Did you set the type of uploaded file as fastq.gz or fastqsanger or left it to auto-detect? If you uploaded a fastq.gz file, you must set it as a fastq.gz type (or the header will change and resulted with an error when running tool). If you correctly set the file as fastq.gz, you must first run Fastq Groomer to change the format to fastqsanger.gz. You can then used it with tools in galaxy.